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Hybrid Genomic Analysis of Salmonella enterica Serovar Enteritidis SE3 Isolated from Polluted Soil in Brazil

Authors :
Danitza Xiomara Romero-Calle
Francisnei Pedrosa-Silva
Luiz Marcelo Ribeiro Tomé
Thiago J. Sousa
Leila Thaise Santana de Oliveira Santos
Vasco Ariston de Carvalho Azevedo
Bertram Brenig
Raquel Guimarães Benevides
Thiago M. Venancio
Craig Billington
Aristóteles Góes-Neto
Source :
Microorganisms, Vol 11, Iss 1, p 111 (2022)
Publication Year :
2022
Publisher :
MDPI AG, 2022.

Abstract

In Brazil, Salmonella enterica serovar Enteritidis is a significant health threat. Salmonella enterica serovar Enteritidis SE3 was isolated from soil at the Subaé River in Santo Amaro, Brazil, a region contaminated with heavy metals and organic waste. Illumina HiSeq and Oxford Nanopore Technologies MinION sequencing were used for de novo hybrid assembly of the Salmonella SE3 genome. This approach yielded 10 contigs with 99.98% identity with S. enterica serovar Enteritidis OLF-SE2-98984-6. Twelve Salmonella pathogenic islands, multiple virulence genes, multiple antimicrobial gene resistance genes, seven phage defense systems, seven prophages and a heavy metal resistance gene were encoded in the genome. Pangenome analysis of the S. enterica clade, including Salmonella SE3, revealed an open pangenome, with a core genome of 2137 genes. Our study showed the effectiveness of a hybrid sequence assembly approach for environmental Salmonella genome analysis using HiSeq and MinION data. This approach enabled the identification of key resistance and virulence genes, and these data are important to inform the control of Salmonella and heavy metal pollution in the Santo Amaro region of Brazil.

Details

Language :
English
ISSN :
20762607
Volume :
11
Issue :
1
Database :
Directory of Open Access Journals
Journal :
Microorganisms
Publication Type :
Academic Journal
Accession number :
edsdoj.5a4d21e7dbc74e23ba1a341237023b57
Document Type :
article
Full Text :
https://doi.org/10.3390/microorganisms11010111